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#!perl
use strict;
use Data::Dumper;
use Carp;
#
# This is a SAS Component
#
HideShow 100 lines of Pod
=head1 query_entity_ObservationalUnit
Query the entity ObservationalUnit.
An ObservationalUnit is an individual plant that 1) is part of an experiment or study, 2) has measured traits, and 3) is assayed for the purpose of determining alleles.  
Example:
    query_entity_ObservationalUnit -a 
=head2 Related entities
The ObservationalUnit entity has the following relationship links:
=over 4
     
=item DefinedBy TaxonomicGrouping
=item HasTrait Trait
=item IsLocated Locality
=item IsPartOf StudyExperiment
=item IsVariedIn Contig
=item UsesReference Genome
=back
=head2 Command-Line Options
=over 4
=item -is field,value
Limit the results to entities where the given field has the given value.
=item -like field,value
Limit the results to entities where the given field is LIKE (in the sql sense) the given value.
=item -op operator,field,value
Limit the results to entities where the given field is related to the given value based on the given operator.
The operators supported are as follows. We provide text based alternatives to the comparison
operators so that extra quoting is not required to keep the command-line shell from 
confusing them with shell I/O redirection operators.
=over 4
=item < or lt
=item > or gt
=item <=  or le
=item >= or ge
=item =
=item LIKE
=back
=item -a
Return all fields.
=item -h
Display a list of the fields available for use.
=item -fields field-list
Choose a set of fields to return. Field-list is a comma-separated list of 
strings. The following fields are available:
=over 4
=item source_name
=item source_name2
=item plant_id
=back    
    
=back
=head2 Output Format
The standard output is a tab-delimited file containing a column
for each requested field.
=cut
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;
#Default fields
my @all_fields = ( 'source_name', 'source_name2', 'plant_id' );
my %all_fields = map { $_ => 1 } @all_fields, 'id';
my $usage = "usage: query_entity_ObservationalUnit [-is field,value] [-like field,value] [-op operator,field,value] [-show-fields] [-a | -f field list] > entity.data";
my $a;
my $f;
my @fields;
my $show_fields;
my @query_is;
my @query_like;
my @query_op;
my %op_map = ('>', '>',
              'gt', '>',
              '<', '<',
              'lt', '<',
              '>=', '>=',
              'ge', '>=',
              '<=', '<=',
              'le', '<=',
              'like', 'LIKE',
              );
my $geO = Bio::KBase::CDMI::CDMIClient->new_get_entity_for_script("a"                => \$a,
                                                                  "show-fields" => \$show_fields,
                                                                  "h"           => \$show_fields,
                                                                  "is=s"        => \@query_is,
                                                                  "like=s"      => \@query_like,
                                                                  "op=s"        => \@query_op,
                                                                  "fields=s"    => \$f);
if ($show_fields)
{
    print STDERR "Available fields: @all_fields\n";
    exit 0;
}
if (@ARGV != 0 || ($a && $f))
{
    print STDERR $usage, "\n";
    exit 1;
}
if ($a)
{
    @fields = @all_fields;
}
elsif ($f) {
    my @err;
    for my $field (split(",", $f))
    {
        if (!$all_fields{$field})
        {
            push(@err, $field);
        }
        else
        {
            push(@fields, $field);
        }
    }
    if (@err)
    {
        print STDERR "all_entities_ObservationalUnit: unknown fields @err. Valid fields are: @all_fields\n";
        exit 1;
    }
}
my @qry;
for my $ent (@query_is)
{
    my($field,$value) = split(/,/, $ent, 2);
    if (!$all_fields{$field})
    {
        die "$field is not a valid field\n";
    }
     
    push(@qry, [$field, '=', $value]);
}
for my $ent (@query_like)
{
    my($field,$value) = split(/,/, $ent, 2);
    if (!$all_fields{$field})
    {
        die "$field is not a valid field\n";
    }
     
    push(@qry, [$field, 'LIKE', $value]);
}
for my $ent (@query_op)
{
    my($op,$field,$value) = split(/,/, $ent, 3);
    if (!$all_fields{$field})
    {
        die "$field is not a valid field\n";
    }
    my $mapped_op = $op_map{lc($op)};
    if (!$mapped_op)
    {
        die "$op is not a valid operator\n";
    }
     
    push(@qry, [$field, $mapped_op, $value]);
}
my $h = $geO->query_entity_ObservationalUnit(\@qry, \@fields );
while (my($k, $v) = each %$h)
{
    print join("\t", $k, map { ref($_) eq 'ARRAY' ? join(",", @$_) : $_ } @$v{@fields}), "\n";
}